It's been several years since I last tried to uninstall/remove Cygwin from a system. At that time, the only way that I could completely and cleanly remove Cygwin was to re-install the OS. Otherwise, I would always seem to find some bits and pieces of Cygwin still on the system. Perhaps they have a better uninstaller now. Anyways, just thought I'd share this in case you might still have some parts of Cygwin hanging around.